SUM’20: State-based user modelling

Capturing and effectively utilising user states and goals is becoming a timely challenge for successfully leveraging intelligent and usercentric systems in differentweb search and data mining applications. Examples of such systems are conversational agents, intelligent assistants, educational and contextual information retrieval systems, recommender/match-making systems and advertising systems, all of which rely on identifying the user state in order to provide the most relevant information and assist users in achieving their goals. There has been, however, limited work towards building such state-aware intelligent learning mechanisms. Hence, devising information systems that can keep track of the user's state has been listed as one of the grand challenges to be tackled in the next few years [1]. It is thus timely to organize a workshop that re-visits the problem of designing and evaluating state-aware and user-centric systems, ensuring that the community (spanning academic and industrial backgrounds) works together to tackle these challenges

Impact of dense-water flow over a sloping bottom on open-sea circulation: Laboratory experiments and an Ionian Sea (Mediterranean) example

The North Ionian Gyre (NIG) displays prominent inversions on decadal scales. We investigate the role of internal forcing induced by changes in the horizontal pressure gradient due to the varying density of Adriatic Deep Water (AdDW), which spreads into the deep layers of the northern Ionian Sea. In turn, the AdDW density fluctuates according to the circulation of the NIG through a feedback mechanism known as the bimodal oscillating system. We set up laboratory experiments with a two-layer ambient fluid in a circular rotating tank, where densities of 1000 and 1015ĝ€¯kgĝ€¯m-3 characterize the upper and lower layers, respectively. From the potential vorticity evolution during the dense-water outflow from a marginal sea, we analyze the response of the open-sea circulation to the along-slope dense-water flow. In addition, we show some features of the cyclonic and anticyclonic eddies that form in the upper layer over the slope area. We illustrate the outcome of the experiments of varying density and varying discharge rates associated with dense-water injection. When the density is high (1020ĝ€¯kgĝ€¯m-3) and the discharge is large, the kinetic energy of the mean flow is stronger than the eddy kinetic energy. Conversely, when the density is lower (1010ĝ€¯kgĝ€¯m-3) and the discharge is reduced, vortices are more energetic than the mean flow - that is, the eddy kinetic energy is larger than the kinetic energy of the mean flow. In general, over the slope, following the onset of dense-water injection, the cyclonic vorticity associated with current shear develops in the upper layer. The vorticity behaves in a two-layer fashion, thereby becoming anticyclonic in the lower layer of the slope area. Concurrently, over the deep flat-bottom portion of the basin, a large-scale anticyclonic gyre forms in the upper layer extending partly toward a sloping rim. The density record shows the rise of the pycnocline due to the dense-water sinking toward the flat-bottom portion of the tank. We show that the rate of increase in the anticyclonic potential vorticity is proportional to the rate of the rise of the interface, namely to the rate of decrease in the upper-layer thickness (i.e., the upper-layer squeezing). The comparison of laboratory experiments with the Ionian Sea is made for a situation when the sudden switch from cyclonic to anticyclonic basin-wide circulation took place following extremely dense Adriatic water overflow after the harsh winter in 2012. We show how similar the temporal evolution and the vertical structure are in both laboratory and oceanic conditions. The demonstrated similarity further supports the assertion that the wind-stress curl over the Ionian Sea is not of paramount importance in generating basin-wide circulation inversions compared with the internal forcing

Guidelines for the functional annotation of microRNAs using the Gene Ontology.

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual).R.P.H. and R.C.L are supported by funding from a British Heart Foundation grant (RG/13/5/30112) and the National Institute for Health Research University College London Hospitals Biomedical Research Centre. M.M. is a Senior Research Fellow of the British Heart Foundation (FS/13/2/29892). A.Z. is an Intermediate Fellow of the British Heart Foundation (FS/13/18/30207). D.S. is supported by a grant awarded to the Mouse Genome Database from the National Human Genome Research Institue at the US National Institutes of Health (HG-00330). P.D’E., M.G., M.O-M. are supported by grants from the US National Institutes of Health (P41 HG003751 and U54 GM114833), Ontario Research Fund, and the European Molecular Biology Laboratory. D.H. is supported by a grant awarded to the Zebrafish Information Network fromthe National Human Genome Research Institute at the US National Institutes of Health (HG002659). A.Z.K. is funded by a NIHR University College London Hospitals Biomedical Research Centre, Research Capability Funding award (RCF) (RCF123). L.M. is a Ragnar Söderberg fellow in Medicine (M-14/55), and received funding from Swedish Heart-Lung-Foundation (20120615, 20130664, 20140186). Huntley, RP 22 R.B. and D.O-S. are supported by R.B. and D.O-S. are supported by a grant awarded to The Gene Ontology Consortium (Principal Investigators: JA Blake, JM Cherry, S Lewis, PW Sternberg and P Thomas) by the National Human Genome Research Institute (NHGRI) (#U41 HG22073). V.P. and J.R.S. are supported by a grant from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health (HL64541). K.V.A. is supported by a grant awarded to the Gene Ontology Consortium from the National Human Genome Research Institute at the US National Institutes of Health (HG002273). V.W. is supported by a Wellcome Trust grant (104967/Z/14/Z). We would like to thank Leonore Reiser and Tanya Berardini who provided guidance on the plant miRNA processing pathway. Also thanks to David Hill, Harold Drabkin, Judith Blake, Karen Christie, Donghui Li and Pascale Gaudet who contributed to discussions regarding GO curation procedures and to Lisa Matthews and Bruce May who provided helpful feedback on the manuscript. We are very grateful to Tony Sawford and Maria Martin from the European Bioinformatics Institute for access to the online GO curation tool, which is an essential component of this annotation project. Many thanks to members of the GO Editorial Office for useful discussions about the placement and definition of new GO terms. We also thank Alex Bateman and Anton Petrov for being responsive to our feedback regarding RNAcentral functionality. Author contributions: R.C.L. initiated discussions in the GO Consortium regarding miRNA curation guidelines and supervised the project, R.P.H. researched and constructed the guidelines and wrote the manuscript, R.P.H., R.C.L., D.S., R.B., P.D’E., M.G., M.O-M., D.H., V.P., J.R.S., K.V.A. and V.W. contributed to discussions regarding GO curation procedures and provided feedback on the manuscript. D.O-S. provided the expertise on definitions and placements of miRNA-related GO terms and performed the necessary updates and additions to both the GO and to the annotation extension relations used herein. M.M., A.Z., L.M. and A.Z.K. provided guidance with the scientific aspect of the guidelines and provided feedback on the manuscript.This is the final version of the article. It first appeared from Cold Spring Harbor Press via http://dx.doi.org/10.1261/rna.055301.11

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits